[BioC] edgeR

Gordon K Smyth smyth at wehi.EDU.AU
Sun Jun 12 00:47:08 CEST 2011

Dear Sumathy,

I don't know whether you're doing anything wrong from a code point of 
view, but you're certainly not giving us enough information in your email. 
We don't know how you've got your results or how you've counted genes <0. 
Basically you need to show us the code you've used.

What genes are you refering to when you say they are "not identified"? 
Why should they have been?

Reading the help page for any edgeR function that performs statistical 
testing, such as decideTestsDGE, will tell you what cutoff values have 
been used.

Best wishes

> Date: 10 Jun 2011 19:33:17 -0500
> From: puvan001 at umn.edu
> To: bioconductor at r-project.org
> Subject: [BioC] edgeR
> I am new to edgeR and I am not a statistician. I analyzed my RNA seq data,
> I got the results as 200 up regulated and 97 down regulated genes. My
> questions are-
> 1. What is the cut off value used by edgeR to say upregulated versus down
> regulated? I am little bit confused here. When I checked the log fold
> changes I couldn't come to a conclusion. When I counted the number of genes
> <0, the number is more than 97. Am I doing some thing wrong?
> 2. If I want to do some pathway analysis, I am wondering which value I have
> to use. When I use log fold change values, some genes are not identified as
> differentially expressed though I gave different cut off values.
> Can somebody help me?
> Sumathy

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